Broadly neutralizing antibodies are the blueprint for variant-proof pansarbecovirus vaccines

A recently Nature Reviews Immunology Study summarized the efficacy of neutralizing antibodies targeting four major regions of the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), namely the receptor-binding domain (RBD) in the S1 subunit, the fusion peptide region in the S2 subunit, the stem helix region and the N-terminal domain.

Review article: Broadly neutralizing antibodies against SARS-CoV-2 and other human coronaviruses. Image credit: Huen Structure Bio/Shutterstock

Different types of coronaviruses

Several pathogenic human coronaviruses (HCoV) have emerged in recent decades, causing epidemics and a pandemic worldwide. Severe acute respiratory syndrome coronavirus (SARS-CoV) first emerged in 2003, Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, and SARS-CoV-2 in 2019, soon to spread around the world spread and led to coronavirus disease in 2019 ( Covid19 Pandemic.

The ancestral SARS-CoV-2 strain essentially evolved into a series of variants categorized as variants of concern (VOC) and variants of interest (VOI). Unfortunately, multiple variants of SARS-CoV-2 have reduced the effectiveness of COVID-19 vaccines, so it is crucial that broadly neutralizing antibodies are developed for both prophylactic and therapeutic purposes.

Although SARS-CoV-2 has a lower case fatality rate than SARS-CoV and MERS-CoV, it has a high infection rate. Corona viruses are part of the family Coronavirida which has been divided into four main genera including alphacoronaviruses (alpha-CoVs), betacoronaviruses (beta-CoVs), gammacoronaviruses (gamma-CoVs) and deltacoronaviruses (delta-CoVs).

Typically, alpha-CoVs and beta-CoVs infect mammals, while gamma-CoVs and delta-CoVs mainly infect avian species. SARS-CoV-2, SARS-CoV, MERS-CoV and HCoVs (HCoV-HKU1 and HCoV-OC43) belong to the betacoronavirus.

Main factors related to viral infections

HCoVs are single-stranded RNA viruses containing phosphorylated nucleocapsid (N) proteins whose cores are encapsulated by phospholipid bilayers to form a spherical particle characterized by the presence of S protein on the outer surface. The S protein contains the S1 and S2 domains, which play key roles in viral infection.

The receptor-binding domain (RBD) of the S1 domain recognizes the host cell’s surface receptors, which is the first step in viral invasion. The S2 domain is responsible for membrane fusion that allows the viral genome to enter the host cell. Two other factors associated with viral infection are furin and transmembrane serine protease 2 (TMPRSS2).

SARS-CoV and SARS-CoV-2 utilize the host’s angiotensin converting enzyme 2 receptor (ACE2), while MERS-CoV uses dipeptidyl peptidase 4 (DPP4) to enter the host cell.

Pathogens are recognized by neutralizing antibodies (nAbs) or non-neutralizing antibodies (non-nAbs). In general, nAbs can more effectively reduce pathogen titers and protect host cells from infection. As mentioned above, the present study mainly focused on the broad neutralizing antibodies (bnAbs) targeting neutralizing epitopes in the N-terminal domain (NTD), stem helix (SH), S1 subunit RBD and fusion peptide (FP ) regions in the S2 subunit.

The NTD

4A8 was recognized as one of the earliest nAbs against NTD. There are five structural loops, ie N1-N5, in the NTD, of which N3 and N5 mediate the interaction with 4A. Other NTD-targeted mAbs include COV2-2676, 5-24, and COV2-2489, which identify epitopes consisting of the N1, N3, and N5 loops.

Many SARS-CoV-2 variants contain mutations within the NTD supersite, reducing the neutralizing potency of NTD supersite-recognizing mAbs. For example, the SARS-CoV-2 beta strain contains a deletion of NTD amino acid residues at 242-244, rendering 4A8, 4-8, and 5-24 ineffective.

The RDB

Most anti-SARS-CoV-2 antibodies target the RBD, which has been divided into different classes based on their target epitopes. The classification by Barnes et al. is most commonly cited, which has divided RBD-directed antibodies into four classes based on their mode of binding to the S protein.

Class 1 and 2 antibodies targeting RBD tend to lose their neutralizing abilities with the emergence of SARS-CoV-2 VOCs carrying new mutations in the RBM. Therefore, their neutralizing breath is limited. In contrast, class 3 and 4 antibodies, which bind to highly conserved epitopes, are more effective in neutralizing SARS-CoV-2 variants and other SARS-like coronaviruses.

In the future, development of a COVID-19 vaccine targeting conserved epitopes could elicit potent broad-spectrum antibodies that could be effective against current and emerging SARS-CoV-2 variants.

The S2 SH region

As mentioned above, the SARS-CoV-2 S protein contains S1 and S2 subunits. The majority of SARS-CoV-2 nAbs target the neutralizing epitopes in the RBD in the S1 subunit and NTD. However, these epitopes are susceptible to mutations that increase the possibility of immune escape by mutant viruses.

Compared to the S1 domain, the neutralizing epitopes are more conserved in the S2 subunit. Therefore, nAbs targeting the S2 epitopes have a greater likelihood of eliciting broad-spectrum nAbs against SARS-CoV-2 and other HCoVs. For example, S2P6 largely neutralizes all beta-CoVs by targeting the S2 subunit.

The S2 FPs

S2 FPs domains are highly conserved across coronavirus genera, indicating the possibility of broad-spectrum antibody induction. Some of the antibodies produced against this epitope showed superior neutralizing activity against Alpha-CoVs, Beta-CoVs, Gamma-CoVs and Delta-CoVs.

COV44-62 and COV44-79 antibodies isolated from convalescent COVID-19 patients could bind the S2-FP region. COV44-62 interacted with the S2 domain of SARS-CoV-2 and neutralized Beta-CoVs and MERS-CoV.